I'm pretty sure that Ubuntu uses the Debian package, which is 2 (nearly 3) versions old. Much has changed internally since, so upgrading will in fact mean that you lose your progress. You can back up your saves before trying the git build, so if you want to go back to the version in Ubuntu's repos you can. Your save files should be located in:

If you edit this file, you should see fullscreen=1 somewhere in there. Change this to 0 and you can play in windowed mode. You might also need to change resolution_w and resolution_h to lower values, since I think this crash has something to do with a limitation in SDL.

We've known about this bug for a while, so I recommend keeping an eye on this Github issue for any fix we might come up with: